Unique gene signatures in cerebrospinal fluid-derived cells from virally suppressed people with HIV

Abstract

Persistent immune response in the central nervous system (CNS) of people living with HIV (PWH), was linked to poor health outcomes and clinical complications. Disease-associated inflammation is often monitored in peripheral blood but may poorly estimate the CNS milieu. Soluble markers in cerebrospinal fluid (CSF) may mark CNS-associated pathology, but are limited to detectable, soluble markers. We demonstrate, in PWH, the utility of immune cell profiling within the CSF, through contrasting three methods. Flow cytometry revealed differences in distinct proportions of select immune cell types between CSF and peripheral blood, with microglia-like cells (P2RY12+) residing only in CSF, and CSF-derived myeloid cells containing a higher proportion of intermediate monocytes. Bulk RNA sequencing showed CSF-derived lymphoid and myeloid cells have gene expression patterns which are distinct from the peripheral blood with many genes showing enrichment for the CSF-derived leukocytes compared to blood. Single-cell RNA sequencing resolved distinct cell-types in the CSF and allowed for cellular decomposition of the CSF-enriched genes identified by bulk RNA sequencing. CSF-enriched genes expressed in bulk myeloid cell were preferentially expressed in the microglia- like subset. While CSF-enriched genes expressed in bulk lymphoid cells were broadly expressed across T-cell subtypes with only select markers showing cellular specificity. Altogether, CSF-derived immune cells from PWH demonstrate a promising, unique CNS gene signature that warrants further study in relation to CNS comorbidities in this clinical population.

Unique gene signatures in cerebrospinal fluid-derived cells from virally suppressed people with HIV

Abstract

Persistent immune response in the central nervous system (CNS) of people living with HIV (PWH), was linked to poor health outcomes and clinical complications. Disease-associated inflammation is often monitored in peripheral blood but may poorly estimate the CNS milieu. Soluble markers in cerebrospinal fluid (CSF) may mark CNS-associated pathology, but are limited to detectable, soluble markers. We demonstrate, in PWH, the utility of immune cell profiling within the CSF, through contrasting three methods. Flow cytometry revealed differences in distinct proportions of select immune cell types between CSF and peripheral blood, with microglia-like cells (P2RY12+) residing only in CSF, and CSF-derived myeloid cells containing a higher proportion of intermediate monocytes. Bulk RNA sequencing showed CSF-derived lymphoid and myeloid cells have gene expression patterns which are distinct from the peripheral blood with many genes showing enrichment for the CSF-derived leukocytes compared to blood. Single-cell RNA sequencing resolved distinct cell-types in the CSF and allowed for cellular decomposition of the CSF-enriched genes identified by bulk RNA sequencing. CSF-enriched genes expressed in bulk myeloid cell were preferentially expressed in the microglia- like subset. While CSF-enriched genes expressed in bulk lymphoid cells were broadly expressed across T-cell subtypes with only select markers showing cellular specificity. Altogether, CSF-derived immune cells from PWH demonstrate a promising, unique CNS gene signature that warrants further study in relation to CNS comorbidities in this clinical population.